User:Amy Kerzmann/Sandbox 100710

Kissing Hairpin Interactions
The structure files shown below were published by Reblova, et al. in the supplementary information portion of their 2003 paper.

View the kissing hairpins in cartoons: 2-bp MMLV, 6-bp HIV-Lai , and 6-bp HIV-Mal.

Analyzing nucleobase stacking interactions


 * Highlight the stack of four unpaired adenine bases of HIV-Lai.
 * Compare with the same positions in HIV-Mal, two of which are guanine instead of adenine.
 * Note that the stack of adenines in HIV-Lai is extrahelical (each base is flipped outside of the helical core).
 * Although the guanine and adenine bases are not stacked in HIV-Mal, those four bases are also extrahelical.

Analyzing electrostatic potential through charge density


 * To examine charge density,highlight phosphate backbone of MMLV 2-bp kiss. Hide the bases for clarity.
 * The backbone of Lai also provides a region of charge density (or high electrostatic potential) to attract cations.